Incidental Mutation 'R0284:Rag2'
ID 24579
Institutional Source Beutler Lab
Gene Symbol Rag2
Ensembl Gene ENSMUSG00000032864
Gene Name recombination activating gene 2
Synonyms Rag-2
MMRRC Submission 038505-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0284 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 101455063-101462874 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 101460464 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 258 (V258A)
Ref Sequence ENSEMBL: ENSMUSP00000106858 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000044031] [ENSMUST00000099682] [ENSMUST00000111227] [ENSMUST00000111231] [ENSMUST00000128898] [ENSMUST00000160037] [ENSMUST00000160722]
AlphaFold P21784
Predicted Effect probably damaging
Transcript: ENSMUST00000044031
AA Change: V258A

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000038204
Gene: ENSMUSG00000032864
AA Change: V258A

DomainStartEndE-ValueType
Pfam:RAG2 51 389 3.5e-179 PFAM
Pfam:RAG2_PHD 414 491 7.2e-50 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000099682
Predicted Effect probably damaging
Transcript: ENSMUST00000111227
AA Change: V258A

PolyPhen 2 Score 0.979 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000106858
Gene: ENSMUSG00000032864
AA Change: V258A

DomainStartEndE-ValueType
Pfam:RAG2 51 389 6.7e-193 PFAM
Pfam:RAG2_PHD 414 491 1.1e-50 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000111231
Predicted Effect probably benign
Transcript: ENSMUST00000128898
Predicted Effect probably benign
Transcript: ENSMUST00000160037
Predicted Effect noncoding transcript
Transcript: ENSMUST00000177171
Predicted Effect noncoding transcript
Transcript: ENSMUST00000177007
Predicted Effect probably benign
Transcript: ENSMUST00000160722
Meta Mutation Damage Score 0.6102 question?
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.1%
  • 10x: 95.9%
  • 20x: 92.4%
Validation Efficiency 100% (61/61)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is involved in the initiation of V(D)J recombination during B and T cell development. This protein forms a complex with the product of the adjacent recombination activating gene 1, and this complex can form double-strand breaks by cleaving DNA at conserved recombination signal sequences. The recombination activating gene 1 component is thought to contain most of the catalytic activity, while the N-terminal of the recombination activating gene 2 component is thought to form a six-bladed propeller in the active core that serves as a binding scaffold for the tight association of the complex with DNA. A C-terminal plant homeodomain finger-like motif in this protein is necessary for interactions with chromatin components, specifically with histone H3 that is trimethylated at lysine 4. Mutations in this gene cause Omenn syndrome, a form of severe combined immunodeficiency associated with autoimmune-like symptoms. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations exhibit arrested development of T and B cell maturation at the CD4-8- thymocyte or B220+/CD43+pro-B cell stage due to inability to undergo V(D)J recombination. [provided by MGI curators]
Allele List at MGI

All alleles(14) : Targeted(14)

Other mutations in this stock
Total: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Alkbh6 A G 7: 30,013,413 (GRCm39) T161A probably benign Het
Alox12e A G 11: 70,211,725 (GRCm39) probably benign Het
Ap1g2 A G 14: 55,339,149 (GRCm39) probably benign Het
Arid2 A T 15: 96,276,848 (GRCm39) probably benign Het
Bmp2k A T 5: 97,216,314 (GRCm39) H604L unknown Het
Cacna1a A T 8: 85,338,914 (GRCm39) M1705L probably damaging Het
Cacna1d A T 14: 29,794,062 (GRCm39) D1526E probably damaging Het
Ccdc171 A G 4: 83,467,975 (GRCm39) R107G possibly damaging Het
Cklf T C 8: 104,988,207 (GRCm39) probably benign Het
Crabp1 A G 9: 54,672,210 (GRCm39) K9E probably benign Het
Cspg4 A G 9: 56,793,423 (GRCm39) D386G probably damaging Het
Cyp3a41b G A 5: 145,515,014 (GRCm39) probably benign Het
Dsg1a T A 18: 20,464,684 (GRCm39) V393E probably damaging Het
Ednrb C T 14: 104,057,449 (GRCm39) G371D probably damaging Het
Efcab5 T C 11: 76,994,353 (GRCm39) probably benign Het
Exoc2 A T 13: 31,061,608 (GRCm39) probably benign Het
Fbn2 G A 18: 58,183,362 (GRCm39) probably benign Het
Foxo6 T C 4: 120,126,199 (GRCm39) S199G probably benign Het
Fpr1 T A 17: 18,097,618 (GRCm39) I124F probably damaging Het
Gk5 A T 9: 96,063,823 (GRCm39) probably null Het
Gys1 A T 7: 45,086,143 (GRCm39) probably benign Het
Igfbp1 T C 11: 7,148,103 (GRCm39) S49P probably damaging Het
Incenp A T 19: 9,871,357 (GRCm39) S91T unknown Het
Itpkc G A 7: 26,913,968 (GRCm39) R498* probably null Het
Kat6a A G 8: 23,429,819 (GRCm39) T1725A unknown Het
Kiz T A 2: 146,705,730 (GRCm39) C97S probably benign Het
Kri1 A G 9: 21,187,848 (GRCm39) probably benign Het
Lipn A G 19: 34,058,106 (GRCm39) S276G possibly damaging Het
Llgl1 A G 11: 60,602,967 (GRCm39) T881A probably damaging Het
Man1a2 T C 3: 100,592,102 (GRCm39) H26R probably damaging Het
Map3k5 T A 10: 19,876,359 (GRCm39) F173I probably damaging Het
Miox C T 15: 89,220,477 (GRCm39) L189F possibly damaging Het
Mipol1 A G 12: 57,503,855 (GRCm39) Q341R probably damaging Het
Mllt6 G T 11: 97,569,431 (GRCm39) A928S probably benign Het
Ncoa6 TGC TGCGC 2: 155,250,211 (GRCm39) probably null Het
Nipsnap3a C T 4: 52,997,178 (GRCm39) T150I probably benign Het
Nsl1 A G 1: 190,797,427 (GRCm39) E97G probably damaging Het
Or11j4 G A 14: 50,630,452 (GRCm39) V80M probably damaging Het
Or4f54 T C 2: 111,122,931 (GRCm39) V106A probably benign Het
Or7g18 A T 9: 18,786,848 (GRCm39) Y72F probably benign Het
Or8c11 G A 9: 38,289,880 (GRCm39) M234I probably benign Het
Pakap T C 4: 57,855,207 (GRCm39) F220L probably damaging Het
Pdcd6ip A G 9: 113,491,572 (GRCm39) L552S probably damaging Het
Plekhf2 T C 4: 10,990,595 (GRCm39) probably benign Het
Prdm1 T C 10: 44,332,622 (GRCm39) E96G probably damaging Het
Prpf40a T A 2: 53,040,659 (GRCm39) E608D probably damaging Het
Prpf40b A T 15: 99,214,274 (GRCm39) probably benign Het
S100a5 A G 3: 90,518,881 (GRCm39) I68V probably benign Het
Serpinb8 G A 1: 107,530,648 (GRCm39) probably null Het
Slc24a4 T C 12: 102,226,740 (GRCm39) V492A probably damaging Het
Spag6l T A 16: 16,598,630 (GRCm39) Q287L probably damaging Het
Spmip6 T G 4: 41,507,538 (GRCm39) E150A probably damaging Het
Synpo2 C T 3: 122,873,383 (GRCm39) W211* probably null Het
Tgtp1 A G 11: 48,877,970 (GRCm39) V245A probably benign Het
Tmem144 G A 3: 79,746,580 (GRCm39) probably benign Het
Trerf1 A G 17: 47,630,471 (GRCm39) noncoding transcript Het
Ttn G C 2: 76,677,048 (GRCm39) probably benign Het
Vmn1r28 G A 6: 58,242,702 (GRCm39) A182T probably benign Het
Vps13d A T 4: 144,871,372 (GRCm39) M1900K probably benign Het
Vps41 A T 13: 19,037,610 (GRCm39) D691V probably damaging Het
Zfp518b T C 5: 38,829,083 (GRCm39) Y974C probably damaging Het
Zscan29 A T 2: 120,997,214 (GRCm39) probably benign Het
Other mutations in Rag2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00647:Rag2 APN 2 101,460,962 (GRCm39) missense probably benign 0.00
IGL01358:Rag2 APN 2 101,460,365 (GRCm39) missense possibly damaging 0.95
IGL01774:Rag2 APN 2 101,460,392 (GRCm39) missense probably damaging 1.00
IGL02267:Rag2 APN 2 101,460,376 (GRCm39) missense probably damaging 1.00
IGL02507:Rag2 APN 2 101,461,055 (GRCm39) missense probably damaging 0.99
IGL02615:Rag2 APN 2 101,459,913 (GRCm39) nonsense probably null
IGL02690:Rag2 APN 2 101,459,839 (GRCm39) missense probably benign 0.00
IGL03087:Rag2 APN 2 101,460,559 (GRCm39) missense probably benign 0.00
IGL03261:Rag2 APN 2 101,460,608 (GRCm39) missense probably damaging 0.96
billfold UTSW 2 101,461,118 (GRCm39) missense probably damaging 1.00
Brag UTSW 2 101,460,040 (GRCm39) missense probably damaging 1.00
excambiar UTSW 2 101,461,121 (GRCm39) missense probably damaging 0.99
picker UTSW 2 101,460,419 (GRCm39) missense probably damaging 1.00
snowcock UTSW 2 101,460,948 (GRCm39) missense probably damaging 1.00
woodcock UTSW 2 101,460,464 (GRCm39) missense probably damaging 0.98
R0266:Rag2 UTSW 2 101,460,948 (GRCm39) missense probably damaging 1.00
R1250:Rag2 UTSW 2 101,460,784 (GRCm39) missense probably damaging 0.96
R1520:Rag2 UTSW 2 101,460,476 (GRCm39) missense probably damaging 0.99
R1641:Rag2 UTSW 2 101,459,960 (GRCm39) missense probably benign 0.22
R2260:Rag2 UTSW 2 101,460,583 (GRCm39) missense probably benign 0.00
R2571:Rag2 UTSW 2 101,460,312 (GRCm39) missense probably damaging 0.99
R3441:Rag2 UTSW 2 101,460,645 (GRCm39) missense probably damaging 0.99
R3752:Rag2 UTSW 2 101,461,121 (GRCm39) missense probably damaging 0.99
R4894:Rag2 UTSW 2 101,460,022 (GRCm39) missense probably damaging 1.00
R5197:Rag2 UTSW 2 101,461,085 (GRCm39) missense probably damaging 1.00
R5236:Rag2 UTSW 2 101,460,005 (GRCm39) missense probably damaging 1.00
R6815:Rag2 UTSW 2 101,460,900 (GRCm39) missense probably damaging 0.99
R7365:Rag2 UTSW 2 101,461,118 (GRCm39) missense probably damaging 1.00
R7917:Rag2 UTSW 2 101,460,040 (GRCm39) missense probably damaging 1.00
R9026:Rag2 UTSW 2 101,460,494 (GRCm39) missense possibly damaging 0.46
R9243:Rag2 UTSW 2 101,460,419 (GRCm39) missense probably damaging 1.00
R9280:Rag2 UTSW 2 101,460,145 (GRCm39) missense probably benign 0.05
R9333:Rag2 UTSW 2 101,460,752 (GRCm39) missense probably benign 0.01
R9500:Rag2 UTSW 2 101,461,217 (GRCm39) missense probably damaging 1.00
X0027:Rag2 UTSW 2 101,460,718 (GRCm39) missense probably damaging 1.00
Z31818:Rag2 UTSW 2 101,461,150 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ATAGTGTAGCTGACTGCCTACCCC -3'
(R):5'- GCCAAGGAAAATAGTCCCGTTTCCC -3'

Sequencing Primer
(F):5'- ATTCTCCCAGAACTTCAGGATGG -3'
(R):5'- GAAAATAGTCCCGTTTCCCATGTTG -3'
Posted On 2013-04-16